# MD Simulation Data for the wild-type (WT) and mutant (MT) complexes of OXA-48, OXA-24/40, OXA-13,  (PDB IDs: 6ZRJ, 7RPE, 1H8Y) 

## Summary
This dataset contains GROMACS parameter files, gmx_MMPB/SA parameter file, ligand topology and parameter files, protein-ligand complex topology, production molecular dynamics simulation files generated by Gromacs and custom index files used for selections in analysis for WT an MT complexes of of OXA-48, OXA-24/40, OXA-13 class D β-lactamases. The data support the findings reported in the manuscript:

**EXPLORING LOCAL FRUSTRATION IN OXA β-LACTAMASES: NEW TARGETS FOR INHIBITOR DEVELOPMENT**  
Authors: Sebnem Ozturk, Pemra Ozbek  
Corresponding Author: [Pemra Ozbek](mailto:pemra.ozbek@marmara.edu.tr)

## Simulation Details

- **Software**: GROMACS 2024  
- **Force field**: CHARMM36 all-atom force field (July 2022 release)  
- **Water model**: CHARMM-modified TIP3P  
- **Ligand topology**: Generated using CGenFF based on the ligand structure obtained from the corresponding PDB entry.

Each simulation includes:
- 100 ns production run 

### Folder tree


├── 6zrj.zip/
│ ├── 6zrj_wt1
  ├── 6zrj_wt2
  ├── 6zrj_wt3
  ├── 6zrj_mt1
  ├── 6zrj_mt2
  ├── 6zrj_mt3

├── 7rpe.zip/
│ ├── 7rpe_wt1
  ├── 7rpe_wt2
  ├── 7rpe_wt3
  ├── 7rpe_mt1
  ├── 7rpe_mt2
  ├── 7rpe_mt3
├── 1h8y.zip/
│ ├── 1h8y_wt1
  ├── 1h8y_wt2
  ├── 1h8y_wt3
  ├── 1h8y_mt1
  ├── 1h8y_mt2
  ├── 1h8y_mt3
├── mdp_files.zip/ # ions.mdp`,`em.mdp`, 'em_conjugategradient.mdp', `nvt.mdp`, `npt.mdp`, `md.mdp` — GROMACS parameter files for each simulation stage
├── mmpbsa.in/ # gmx_MMPB/SA parameter file
└── README.md

Each `*_md/` directory contains production-stage MD outputs and the topology/index files required for analysis:
- `lig.itp`, `lig.prm` — Ligand topology and parameter files generated with CGenFF  


Each `*wt_1,2/` and `*mt_1,2/` directory contains production-stage MD outputs and the topology/index files required for analysis:
- `*_100.tpr` — Production trajectory ` — GROMACS run input file (contains all topology and MD parameters)  
- `*_100.xtc` — Production trajectory   
- `*_100.gro` — Initial structure   
- `*.ndx` — Custom index file used for selections in analysis  
- `*.top` — System topology file  
- `*lig.itp` — Ligand include topology file  
- `*lig.prm` — Ligand force field parameter file  


Citation

If you use this dataset, please cite the associated publication (DOI will be added upon acceptance):

    
License

This dataset is shared under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
